(For those new to the column, Forward Migration is our term for companies moving from Wintel machines to Macs — or at least adding or increasing the number of Macs they use. A forward migration kit is an overview of Mac OS products for a particular occupation, such as dentistry, accounting, etc.)
Today we’re starting a multi-part series on biotechnology products for the Mac OS. The products mentioned were found at Apple’s Macintosh Products Guide (an invaluable resource that you should check out) or sent to us by MacCentral readers.
ABI PRISM EditView by PE Applied Biosystems is a tool for assisting genetic researchers in mapping out the entire human genetic structure. This Mac-only application is a free sequence viewer that allows viewing and printing of analyzed sample files containing DNA sequences.
Ambicode for Mac OS X is an editor to select subsets of genetic code and choose wobble amino acids with reduced degeneracy. It’s useful for designing random oligos with particular amino acid representation. (Thanks to Eric Cherry for the heads-up on this one.)
Caduceus MCAT by Scientia offers an integrated review of physics, chemistry, biology and organic chemistry following the official published MCAT syllabus. There’s a dynamic index for moving between subjects.
DIAS (Dynamic Image Analysis System) by Solltech is “the most advanced computer system commercially available for analyzing how cells move and change shape over time,” say the folks at Solltech. It contains both manual and automatic digitization modes, advanced image-processing capabilities, the ability to quantify more than 30 parameters of motion and dynamic morphology, the capacity to generate a variety of dynamic movies demonstrating motility and dynamic morphology, and sophisticated graphing and analytical capabilities.
DNA Strider is a software program designed to automate and simplify analysis of DNA sequences. Version1.3 is available for purchase directly from its author, Dr. Christian Marck. It’s a favorite of Sylvain Foisy, Ph.D, Centre hospitalier de l’Universite de Montreal.
“It used to be freeware (version 1.0.1), but since version 1.2, it has cost US$200 — and its’ still a bargain,” Foisy said. “It is still the fastest, meanest software to do restriction enzyme analysis of DNA sequences. Its main limitation: a limit of 200 enzymes that can be included in its REList file.”
Embase by SilverPlatter Information is a comprehensive pharmacological and biomedical database with drug information retrieved from 3500 journals from 110 countries.
FlowJo by Tree Star is software used to process hundreds of samples, and create comprehensive tables and graph layouts. “Flowjo is the best facs analysis software, and it is only available for the Mac,” said Art Salomon of the Genomics Institute of the Novartis Research Foundation in San Diego, CA. “It was developed by Mario Roederer at Stanford and Treestar Software. This software is used extensively in the field of immunology and is essential for many other fields. There simply is no other product that compares to this one.”
Gene Construction Kit by Textco has sophisticated plasmid drawing and DNA manipulation capabilities. DNA can be viewed graphically or as text, restriction sites automatically marked, and regions of interest shown. Multiple constructs can be displayed simultaneously.
GCK 2.5 will be available for beta testing at Textco’s Web site in a few days, according to Textco spokesperson Roberta Brucks Gross. The Mac version of GCK 2.5 has a new Aqua interface and is Carbonized for Mac OS X; it will run on Mac OS 8.6 or higher. The upgraded version will also have a “Deluxe Importer” Module that will download and convert standard GenBank DNA sequence files — as well as standard EMBL DNA sequence files — into GCK2 graphical constructs, along with powerful web database searching capabilities.
Gene Inspector, also by Textco, allows biologists to follow their thought processes as they analyze sequences and take notes on their Mac. Interactive analyses allow researchers to pursue intriguing results by using one analysis result to start another one. Analysis suites can be defined and accessed easily. GI also provides an electronic laboratory notebook to archive and annotate experimental results.
GeneJockey by Biosoft is a multi-window package for editing, manipulating and analyzing nucleic acid and protein sequences. It generates optimized PCR primers, selects all possible pairs of oligonucleotides suitable for use as primers to direct efficient DNA amplification by the polymerase chain reaction.
HYBsimulator by Advanced Gene Computing Technologies is a utility for creating all oligonucleotide sequences for a target gene.
Lasergene by DNASTAR, Inc. is a DNA protein and analysis system.
Life Forms 3.0 by Credo Interactive Inc. is a tool for making 3D character movement. It provides a workspace for creating character movement and editing motion capture data.
MacLogP by BioByte Corp. has an enlarged database of names, structures and biological activities, as well as advanced searching capability. Calculating the hydrophobic parameter, log P (octanol), it uses algorithms based on 25 years of research by Corwin Hansch and Albert Leo in the QSAR field. MacLogP 2.0 can directly import and export data in “MOL” file, allowing easy exchange with MDL’s ISIS/Draw and CSC’s ChemDraw.
MacPhrap by CodonCode Corp. is an integrated, Power-PC native version of Phil Green’s programs Phred, Cross_match, and Phrap. It provides Phred’s base calling with base-specific quality scores, crossmatches the ability to rapidly compares sets of DNA sequences and to perform vector screening, and Phrap’s performance in generating assemblies from shotgun sequencing projects without the need for “clipping.”